The dynamics of N⁶-methyladenine RNA modification in interactions between rice and plant viruses

N⁶-methyladenosine (m⁶A) is the most common RNA modification in eukaryotes and has been implicated as a novel epigenetic marker that is involved in various biological processes. The pattern and functional dissection of m⁶A in the regulation of several major human viral diseases have already been reported. However, the patterns and functions of m⁶A distribution in plant disease bursting remain largely unknown.

We analyse the high-quality m⁶A methylomes in rice plants infected with two devastating viruses. We find that the m⁶A methylation is mainly associated with genes that are not actively expressed in virus-infected rice plants. We also detect different m⁶A peak distributions on the same gene, which may contribute to different antiviral modes between rice stripe virus or rice black-stripe dwarf virus infection. Interestingly, we observe increased levels of m⁶A methylation in rice plant response to virus infection. Several antiviral pathway-related genes, such as RNA silencing-, resistance-, and fundamental antiviral phytohormone metabolic-related genes, are also m⁶A methylated. The level of m⁶A methylation is tightly associated with its relative expression levels.

We revealed the dynamics of m⁶A modification during the interaction between rice and viruses, which may act as a main regulatory strategy in gene expression. Our investigations highlight the significance of m⁶A modifications in interactions between plant and viruses, especially in regulating the expression of genes involved in key pathways.